An approach to Schubert calculus is to realize Schubert classes as concrete combinatorial objects such as Schubert polynomials. Using the polytope ring of the Gelfand–Tsetlin polytopes, Kiritchenko–Smirnov–Timorin realized each Schubert class as a sum of reduced Kogan faces. The first named author introduced a generalization of reduced Kogan faces to symplectic Gelfand–Tsetlin polytopes using a semi-toric degeneration of a Schubert variety, and extended the result of Kiritchenko–Smirnov–Timorin to type C case. In this paper, we introduce a combinatorial model to this type C generalization using a kind of pipe dream with self-crossings. As an application, we prove that the type C generalization can be constructed by skew mitosis operators.